1. Chang DT, Ke CH, Lin JH, Chiang JH. AutoBind: Automatic extraction of protein-ligand binding affinity data from biological literature. Bioinfomatics. 2012; 28:2162-8.

2. Lee YC, Yang YC, Huang CL, Kuo TY, Lin JH, Yang DM, Huang NK. When cytokinin, a plant hormone, meets the adenosine A2A receptor: A new neuroprotectant and lead for treating neurodegenerative disorders?. PLoS ONE. 2012; 7:e38865.

3. Wang JC, Chu PY, Chen CM, Lin JH*. idTarget: a web server for identifying proteins targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. Nucleic Acids Res. 2012; 40:W393.

4. Deore RR, Chen GS, Chang PT, Chern TR, Lai SY, Chuang MH, Lin JH, Kung FL, Chen CS, Chiou CT, Chern JW. Discovery of N-Arylalkyl-3-hydroxy-4-oxo-3,4-dihydroquinazolin-2-carboxamide derivatives as HCV NS5B polymerase inhibitors. ChemMedChem. 2012; 7:850.

5. Lin JH. Accommodating protein flexibility for structure-based drug design. Curr Top Med Chem. 2011; 11:171-178.

6. Wang JC, Lin JH*, Chen CM, Perryman AL, Olson AJ. Robust scoring functions for protein-ligand interactions with quantum chemical charge models. J Chem Inf Model. 2011; 51:2528.

7. Romera C, Bombarde O, Bonnet R, Gomez D, Dumy P, Calsou P, Gwan JF, Lin JH, Defrancq E, Pratviel G. Improvement of porphyrins for G-quadruplex DNA targeting. Biochimie. 2011; 93:1310.

8. Lin YS, Lin JH*, Chang CC. Molecular dynamics simulations of the rotary motor Fo under external electric fields across the membrane. Biophys J. 2010; 98:1009-1017.

9. Yang PM, Lin JH, Huang WY, Lin YC, Yeh SH, Chen CC. Inhibition of histone deacetylase activity is a novel function of antifolate drug methotrexate. Biochem Biophys Res Comm. 2010; 391:1396-1399.

10. Huang WJ, Huang CC, Hsin LW, Tsai YM, Lin CT, Lin JH, Lee SS. Improved enamine-type addition of dehydroaporphine using microwave irradiation. Tetrahedron Lett. 2010; 51:3062-3064.

11. Chang DT, Lin JH, Hsieh CH, Oyang YJ. On the design of optimization algorithms for prediction of molecular interactions. Int J Art Intell Tools. 2010; 19:267-280.

12. Wang JC, Lin JH*. Robust regression analysis of protein-ligand binding free energy models: toward identification of druggable genomes. Int J Syst Syn Biol. 2010; 1:339-354.

13. Lee PH, Kuo KL, Chu PY, Liu WM, Lin JH*. SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters. Nucleic Acids Res. 2009; 37:W559-W564.

14. Yi-Chu Lin, Jung-Hsin Lin, Chia-Wei Chou, Yu-Fan Chang, Shu-Hao Yeh, and Ching-Chow Chen. Statins Increase p21 through Inhibition of Histone Deacetylase Activity and Release of Promoter-Associated HDAC1/2. Cancer Res. 2008; 68:2375-2383(SCI)

15. S.-S. Lee, U. Venkatesham, C. P. Rao, S.-H. Lam, J.-H. Lin. Preparation of Secolycorines against Acetylcholinesterase. Bioorganic & Medicinal Chem. 2007; 15:1034(SCI)

16. Rommie E. Amaro, David D. L. Minh, Lily S. Cheng, William M. Lindstrom, Jr., Arthur J. Olson, Jung-Hsin Lin, Wilfred W. Li and J. Andrew McCammon. Remarkable Loop Flexibility in Avian Influenza N1 and its Implications for Antivirial Drug Design. J. Am. Chem. Soc. 2007; 129:7764-7765(SCI)

17. A. L. Perryman, J.-H. Lin, J.A. McCammon. Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design. Chem. Biol. Drug Design 2006; 67:336-345

18. D. T.-H. Chang, Y.-Z. Weng, J.-H. Lin, M.-J. Hwang, Y.-J. Oyang. Promtemot: prediction of protein binding sites with automatically extracted geometrical templates. Nucleic Acids Res. 2006; 34:W304-W309

19. A. L. Perryman, J.-H. Lin, J.A. McCammon. Restrained molecular dynamics of HIV-1 protease: Validating a new target for drug design.. Biopolymers 2006; 82:272-284(SCI)

20. D. Vigil, J.-H. Lin, C. A. Sotriffer, J. K. Pennypacker, J.A. McCammon and S. S. Taylor. A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP. Prot. Sci. 2006; 15:113-121

21. J. R. Giorgione, J.-H. Lin, J.A. McCammon and A. C. Newton. Increased membrane affinity of the C1 domain of protein kinase Cdelta components for the lack of involvement of its C2 Domain in membrane recruitment.. J. Biol. Chem. 2006; 281:1660-1669

22. D. T.-H. Chang, Y.-J. Oyang, J.-H. Lin. MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. Nucleic Acids Res. 2005; 33:W233-W238

23. A. L. Perryman, J.-H. Lin, J.A. McCammon. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new drug target site for drugs. Prot. Sci. 2004; 13:1108-1123

24. J.-H Lin*, A. L. Perryman, J. R. Schames and J. A. McCammom. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003; 68:47-62

25. J.-H Lin*, N. A. Baker and J. A. McCammom. Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophys. J. 2002; 83:1374-1379

26. J.-H Lin*, A. L. Perryman, J. R. Schames and J. A. McCammom. Computational drug design acommodating receptor flexibility: The relaxed complex scheme. J. Am. Chem. Soc. 2002; 124:5632-5633

27. J.-H. Lin, and A. Baumgaertner.. Stability of a melittin pore in a lipid bilayer : a molecular dynamics study.. Biophys. J. 2000; 78:1714-1724

28. J.-H. Lin, and A. Baumgaertner.. Molecular dynamics simulations of hydrophobic and amphiphatic proteins interacting with a lipid bilayer membrane.. Comput.Theor.Poly.Sci. 2000; 10(1-2):97-102

29. J.-H. Lin, and A. Baumgaertner.. Adsorption of melittin to a lipid bilayer : a molecular dynamics study.. J. Mol. Liquids. 1999; 84(1):89-98